Variant report

Variant	rs9405861
Chromosome Location	chr6:5699100-5699101
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:5698456-5699217	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr6:5698521-5699176	ECC-1	luminal epithelium:	n/a	chr6:5699139-5699149
3	NFIC	chr6:5698517-5699265	ECC-1	luminal epithelium:	n/a	n/a
4	EP300	chr6:5698373-5699736	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5693144..5695686-chr6:5698907..5701640,2	K562	blood:

Variant related genes	Relation type
ENSG00000270174	TF binding region
ENSG00000270174	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11752777	0.84[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs13213128	0.89[CHB][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2005970	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2142738	0.85[CHB][hapmap]
rs2326634	0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4959347	0.89[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4960125	0.95[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4960126	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62408067	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs760675	0.84[CHB][hapmap]
rs7746913	0.90[CHB][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs877010	0.95[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9378979	0.84[CHB][hapmap]
rs9378980	0.95[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9392709	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9392710	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9405278	0.81[ASN][1000 genomes]
rs9405280	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9405281	0.89[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9405859	0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs9504488	0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3473790	chr6:5692573-5707035	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv3473791	chr6:5692573-5707035	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv823407	chr6:5692735-5706712	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv970201	chr6:5693538-5699453	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5672200-5705800	Weak transcription	Thymus	Thymus
2	chr6:5673800-5701200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr6:5673800-5709800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:5678000-5709400	Weak transcription	Pancreas	Pancrea
5	chr6:5684800-5706000	Weak transcription	Ovary	ovary
6	chr6:5692800-5701400	Weak transcription	Right Atrium	heart
7	chr6:5695200-5700000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:5695800-5699600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:5695800-5709800	Weak transcription	Fetal Stomach	stomach
10	chr6:5696200-5699200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:5696200-5699400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:5696200-5707600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:5696200-5712400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:5696400-5699200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:5696400-5705400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:5697400-5699200	Weak transcription	Primary T cells from cord blood	blood
17	chr6:5697600-5700800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:5698000-5700400	Enhancers	Primary B cells from cord blood	blood
19	chr6:5698200-5699400	Enhancers	Spleen	Spleen
20	chr6:5698200-5700000	Enhancers	Primary B cells from peripheral blood	blood
21	chr6:5698200-5700400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr6:5698400-5699400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:5698400-5699400	Enhancers	Esophagus	oesophagus
24	chr6:5698400-5699600	Enhancers	GM12878-XiMat	blood
25	chr6:5698600-5699200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:5698600-5699400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:5698800-5700200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr6:5698800-5700400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr6:5699000-5699200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:5699000-5699200	Enhancers	Fetal Thymus	thymus
31	chr6:5699000-5699600	Enhancers	Dnd41	blood
32	chr6:5699000-5699800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:5699000-5701200	Weak transcription	Fetal Muscle Trunk	muscle

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